Troubleshooting¶

If you encounter issues while using the TOSTADAS pipeline, refer to the following troubleshooting steps to resolve common problems:

Common Issues and Solutions¶

1. Errors with 'table2asn not on PATH' or a Python library missing when using the singularity or docker profiles¶

Issue: Nextflow is using an outdated cached image.

Solution: Locate the image (e.g., $HOME/.singularity/staphb-tostadas-latest.img) and delete it. This will force Nextflow to pull the latest version.

2. Pipeline hangs indefinitely during the submission step, or you get a "duplicate BioSeq ID error"¶

Issue: This may be caused by duplicate sample IDs in the FASTA file (e.g., a multicontig FASTA). This is only a problem for submissions to Genbank using table2asn.

Solution: Review the sequence headers in the sample FASTA files and ensure that each header is unique.

Get in Touch¶

If you need to report a bug, suggest new features, or just say “thanks”, open an issue and we’ll try to get back to you as soon as possible!